3RMB | pdb_00003rmb

Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DY4	pdb entry 2DY4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	297	6.5 % PEG 2000 MME, 100 mM Na acetate, 150 mM MgSO4, 100 mM Hepes pH 7.2, 6% glycerol and 2 mM beta-mercaptoethanol, vapor diffusion, hanging drop, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.528	α = 90
b = 123.439	β = 96.84
c = 164.291	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY	2006-08-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.991873	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.65	50	98.4	0.076	15.5	3.9		151989

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.65	2.74	87.9		0.458		2.6	13542

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		pdb entry 2DY4	2.65	50	1	148184	25473	91.5	0.2242	0.22	0.2763	0.27	RANDOM	70.1773

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
4.541		9.709	-5.908		1.367

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	2.951
c_mcangle_it	2.39
c_scbond_it	1.863
c_mcbond_it	1.382
c_angle_d	1.218
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	29065
Nucleic Acid Atoms	2596
Solvent Atoms	500
Heterogen Atoms	5

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.